Update 2: I saved and reloaded. Problem is back! Lets see if I can find the specific thing that is breaking.
I kind of wonder if it is the yeeting into the void, and I have gone around to all my island groups and I have nothing else yeeting off an island. But there is a bit of a couple weird things.
So weird thing one. The Hub is doing it now. I tried zooming way in as i have a couple groups of islands around the hub, both directly adjacent and a couple squares nearby. It looks like it mostly just happens when the Hub island is within view.
Weird thing two. The island group that originally seemed to be breaking has some belts yeeting into the void. When I went back and looked at it, the belts that lead up to the void are empty. I followed it back and there is a portion of my factory setup where the belts that should have shapes on them actually don't.
Like everything is moving, but there is an invisible wall blocking the shapes from going. Thankfully pausing the game stops the flickering so I was able to screenshot the "invisible wall." It is even even across all three belts. There is even weird straglers on the stackers.
So, when I unpause I can see the belts moving, but the shapes don't move as if they are backed up, yet there is no shapes on the factory setup itself.
Weird thing three. After finding the previous thing I went back and looked for something similar on the Hub since it was starting to do this same flickering. I found two problem spots, both of which are fluid unpackers. It seems like they aren't registering that there is a fluid block on them at all, but that seems to be the only problem with that. There is no invisible wall at all since the blocks are on the unpackers. Both packers look the same so just screenshot one.
It is really hard to get a screenshot of the flickering because it either comes out fine, or it comes out with the islands just gone. But I can say that the moment it goes from minimal flickering to really bad flickering is the point in zoom where the textures go from basic minimalistic shapes, to detailed shapes. (forth screenshot)
But for now, that is all I could figure out. I feel like the first island is where the problem started, and not the Hub. I went back and tested the I clear since I remembered I should. xD Everything from the islands cleared except for the portion in the fifth screenshot. I paused, deleted that island, and found a handful of shapes still hanging around. Unpausing made them disappear, but the issue was still persisting on the Hub.